Reactome
Reactome (reactome.org ) is an open source, manually curated and peer-reviewed database of reactions and biological interactions. In this particular context, the term "Reactome" is used to refer to the entire repertoire of possible interactions, given the genetic make-up of an organism [1 ] [2 ]. The database is maintained on a quarterly system as well as peer-reviewed by molecular biologists in collaboration with the Reactome editorial staff. Moreover, the content is cross-referenced with other biological-databases such as UniProt, NCBI EntrezGene, Ensembl, UCSC, HapMap, KEGG Compound and ChEBI, while referencing primary research literature from PubMed and GO. Each entity in the database represents a protein, a gene or a molecular complex, allowing for searches across a spectrum of cellular functions. As of 2010 the database contains 5272 human proteins, 3847 reactions,1057 pathways and 3504 macromolecular complexes [3 ]. __TOC__ Usage Reactome provides its users with a web-based platform, which is intuitive and friendly to navigate. Moreover, the authors have provided a user guide wiki (wiki.reactome.org) with detailed instructions as well as a series of videos (see video below) showing the completion of specific tasks on the database. Below is an example of searching the database with a particular query, which in this case is "transferrin". - If interested in the pathway of iron uptake in humans, one could start by querying: transferrin. As Figure 1 shows, the first database entry found seems highly relevant to our search and it is clear that it is recently updated (around 3 months ago from the time of this contribution). - Once we click on the link we find most relevant to our search, we obtain the results illustrated in Figure 2. The green squares show the key reactions in the pathway. - We can zoom-in for a higher resolution of the Transferrin pathway (Figure 3). We can now see that the reactions highlighted by the green squares corespond to Binding reactions (on the cell membrane), dissociation reactions and catalysis (on the endosome). - Furthermore, the raw data presented in digrams can be downloaded as a table in various formats. Reactome in the Literature The Reactome database has been used to map various pathways to intellectual disability in Down syndrome [4 ] and other pathways involved in cancer, and prostrate cancer in particular [5 ]. Other studies have used Reactome for genome-wide approaches to identifying important molecules in pathogen-host interactions [6 ]. References 1. Joshi-Tope, G., et al. (2005). "Reactome: a knowledgebase of biological pathways." Nucleic Acids Res 33(Database issue): D428-432. 2. Matthews, L., et al. (2009). "Reactome knowledgebase of human biological pathways and processes." Nucleic Acids Res 37(Database issue): D619-622. 3. Croft, D., et al. (2011). "Reactome: a database of reactions, pathways and biological processes." Nucleic Acids Res 39(Database issue): D691-697. 4. Gardiner, K., et al. (2010). "Down syndrome: from understanding the neurobiology to therapy." J Neurosci 30(45): 14943-14945. 5. Wang, J., et al. (2012). "B-Raf activation cooperates with PTEN loss to drive c-Myc expression in advanced prostate cancer." Cancer Res 72(18): 4765-4776. 6. Karlas, A., et al. (2010). "Genome-wide RNAi screen identifies human host factors crucial for influenza virus replication." Nature 463(7282): 818-822.